Is SOBP p.Pro472= (c.1416C>A) pathogenic?

SOBP p.Pro472= (c.1416C>A) is classified Benign/Likely benign in SOBP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-07-19). Low-frequency (popmax 1.61%, sas); Associated with intellectual disability, anterior maxillary protrusion, and strabismus.

What condition is associated with SOBP p.Pro472= (c.1416C>A)?

SOBP p.Pro472= (c.1416C>A) is associated with intellectual disability, anterior maxillary protrusion, and strabismus (ClinVar).

How common is SOBP p.Pro472= (c.1416C>A) in the general population?

SOBP p.Pro472= (c.1416C>A) is low-frequency (popmax 1.61%, sas) (gnomAD).

SOBP p.Pro472=

c.1416C>A · rs369211430 · VCV212277

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.61%, sas)

Conditions

intellectual disability, anterior maxillary protrusion, and strabismus

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -2.4
Overall
CADD	6.708	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.61% South Asian · 1,407/87,274 alleles

Filtering AF 1.54% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.51%

Overall 0.174% 2,726/1,567,312 alleles · low-frequency exomes 2,541/1,415,126 · genomes 185/152,186 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	1.61%	62
Ashkenazi Jewishnot grpmax-eligible	1.11%	90
Middle Eastern	0.992%	101
Remaining individualsnot grpmax-eligible	0.273%	366
Admixed American	0.107%	932
European (non-Finnish)	0.0599%	1,669
African / African-American	0.0149%	6,722
East Asian	0.00473%	21,147
Finnishnot grpmax-eligible	0.00212%	47,094

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SOBP
Protein: p.Pro472=
Coding: c.1416C>A
MANE Select: NM_018013
dbSNP: rs369211430
Type: single nucleotide variant
Location: chr6:107634260 (GRCh38)
Gene constraint: LOEUF 0.191 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 52.41
Residue 472: the 'disordered' region

Full SOBP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, anterior maxillary protrusion, and strabismus — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SOBP p.Ala208Thr Uncertain significance ★★ ⚠ same condition
SOBP p.Pro139Ser Uncertain significance ★★ ⚠ same condition
SOBP p.Pro441Ser Uncertain significance ★★ ⚠ same condition
SOBP p.Pro577Ser Uncertain significance ★★ ⚠ same condition
SOBP p.Ser683Gly Benign ★★ same condition
SOBP c.574-3C>T Uncertain significance ★ same condition
SOBP p.Asn721Lys Uncertain significance ★ ⚠ same condition
SOBP p.Gln604Lys Conflicting classifications of pathogenicity ★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/sobp-p-pro472 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown